If you hit a key fast enough during boot, it should drop you into the u-boot prompt instead of booting the kernel.
Contained in the update file: kobo-upgrade-1.8.zip (or the older kobo-upgrade-1.4.zip):
fs.img
u-boot.bin-eb600em
uImage-eb600em
So, you should be able to use RandomInsano's technique to load the files into memory and then write to flash. Your kernel is booting already, so I would do the fs.img first and see if the kobo will boot all the way. Keep in mind that the fs.img itself contains another upgrade file that gets loaded by /etc/init.d/rcS.
The structure of the internal flash shown during boot as:
Creating 7 MTD partitions on "NAND 1GiB 3,3V 8-bit":
0x00000000-0x00080000 : "uboot"
0x00080000-0x00260000 : "kernel"
0x002e0000-0x003a0000 : "picture"
0x003a0000-0x003c0000 : "parameters"
0x003c0000-0x0a3c0000 : "rootfs"
0x0a3c0000-0x0a4c0000 : "app"
0x0a4c0000-0x40000000 : "other"
If you want to test whether your existing kernel will work with the fs.img in the kobo-upgrade-1.x.zip without committing to writing it to internal flash, you can boot the rootfs from an SD card (I did this with a 1GB SD card I have lying around).
1) On a Linux (and presumably a Mac - but I don't know Mac) PC, create an ext3 partition on the SD card.
a) For the PC, get yaffshiv (a python script to extract the yaffs filesystem from fs.img).
https://github.com/devttys0/yaffshiv
I used:
yaffshiv -a -f fs.img -d ./rootfs
b) Mount the SD card with the ext3 partition and copy the contents of the extracted yaffs filesystem to the root of the SD card:
cd rootfs
cp -P -r * /path/to/mounted/sdcard
2) With the kobo off and FTDI attached, put the SD card into the kobo
3) Here you have two choices:
a) Hold down the center D-pad button while powering on and watch the boot messages. Chances are it will boot all the way.
b) Hit a key during u-boot. Then, type bootsd. Watch the boot messages. Chances are it will boot all the way.
4) At this point, check to see if the /mnt/onboard structure exists:
# cd /mnt/onboard
# ls -la
drwxr-xr-x 5 root root 4096 Jan 1 1970 .
drwxr-xr-x 1 root root 2048 Jan 1 1970 ..
drwxr-xr-x 2 root root 4096 Apr 8 2009 .adobe-digital-editions
drwxr-xr-x 9 root root 8192 Mar 20 2017 .kobo
drwxr-xr-x 4 root root 4096 Apr 8 2009 Desktop Installers
-rwxr-xr-x 1 root root 298 Feb 19 07:46 bookmarks
-rwxr-xr-x 1 root root 3761 Feb 19 07:46 books
This gets mounted by /etc/init.d/rcS from mtdblock6.
If booted from SD card:
# mount
rootfs on / type rootfs (rw)
/dev/root on / type ext3 (rw,data=ordered)
none on /proc type proc (rw)
none on /tmp type tmpfs (rw)
none on /var/log type tmpfs (rw)
none on /var/run type tmpfs (rw)
none on /sys type sysfs (rw)
/dev/mtdblock6 on /mnt/onboard type vfat (rw,fmask=0022,dmask=0022,codepage=cp437,iocharset =utf8)
Compare to booted from flash:
# mount
rootfs on / type rootfs (rw)
/dev/root on / type yaffs (rw) <= the only difference!
none on /proc type proc (rw)
none on /tmp type tmpfs (rw)
none on /var/log type tmpfs (rw)
none on /var/run type tmpfs (rw)
none on /sys type sysfs (rw)
/dev/mtdblock6 on /mnt/onboard type vfat (rw,fmask=0022,dmask=0022,codepage=cp437,iocharset =utf8)
Hopefully, the previous bad upgrade did not delete or corrupt mtdblock6 (it should not have touched these parts of the flash). If this is missing, you will need the mtdblock6 image. Otherwise, you should have a fully functional Kobo if the upgrade rootfs is compatible with the older kernel and u-boot.